> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench.md). # Workbench - [Introduction](https://docs.omics.ai/products/workbench/introduction.md) - [Getting Started](https://docs.omics.ai/products/workbench/getting-started.md) - [Logging into Workbench](https://docs.omics.ai/products/workbench/getting-started/log-into-workbench.md) - [Connecting an Engine](https://docs.omics.ai/products/workbench/getting-started/connect-an-engine.md) - [Finding or Importing a Workflow](https://docs.omics.ai/products/workbench/getting-started/finding-or-importing-a-workflow.md) - [Configuring Workflow Inputs](https://docs.omics.ai/products/workbench/getting-started/configuring-workflow-inputs.md) - [Running and Monitoring a Workflow](https://docs.omics.ai/products/workbench/getting-started/submitting-and-monitoring-a-workflow-run.md) - [Locating Outputs](https://docs.omics.ai/products/workbench/getting-started/locating-workflow-outputs.md) - [Reviewing Analysis](https://docs.omics.ai/products/workbench/getting-started/reviewing-analysis.md) - [Engines](https://docs.omics.ai/products/workbench/engines.md) - [Adding and Updating an Engine](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine.md) - [On AWS HealthOmics](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/aws-healthomics.md) - [On Microsoft Azure](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/microsoft-azure.md) - [On Google Cloud Platform](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/google-cloud-platform.md) - [On Premises](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/on-premises.md) - [Parameters](https://docs.omics.ai/products/workbench/engines/parameters.md) - [AWS HealthOmics](https://docs.omics.ai/products/workbench/engines/parameters/aws-healthomics.md) - [Google Cloud Platform](https://docs.omics.ai/products/workbench/engines/parameters/google-cloud-platform.md) - [Microsoft Azure](https://docs.omics.ai/products/workbench/engines/parameters/microsoft-azure.md) - [On-Premises](https://docs.omics.ai/products/workbench/engines/parameters/on-premises.md) - [Cromwell](https://docs.omics.ai/products/workbench/engines/parameters/cromwell.md) - [Amazon Genomics CLI](https://docs.omics.ai/products/workbench/engines/parameters/amazon-genomics-cli.md) - [Workflows](https://docs.omics.ai/products/workbench/workflows.md) - [Finding Workflows](https://docs.omics.ai/products/workbench/workflows/discovering-workflows.md) - [Adding a Workflow](https://docs.omics.ai/products/workbench/workflows/adding-a-workflow.md) - [Support Files](https://docs.omics.ai/products/workbench/workflows/support-files.md): Bundle transformations, defaults, and dependencies alongside your workflow files - [Supported Languages](https://docs.omics.ai/products/workbench/workflows/supported-languages.md) - [Repositories](https://docs.omics.ai/products/workbench/workflows/repositories.md) - [Dockstore](https://docs.omics.ai/products/workbench/workflows/repositories/dockstore.md) - [Instruments](https://docs.omics.ai/products/workbench/instruments.md) - [Getting Started with Instruments](https://docs.omics.ai/products/workbench/instruments/getting-started-with-instruments.md) - [Connecting a Storage Account](https://docs.omics.ai/products/workbench/instruments/connecting-a-storage-account.md) - [Using Sample Data in a Workflow](https://docs.omics.ai/products/workbench/instruments/using-sample-data-in-a-workflow.md) - [Running Workflows Using Samples](https://docs.omics.ai/products/workbench/instruments/running-workflows-using-samples.md) - [Family Based Analysis with Pedigree Information](https://docs.omics.ai/products/workbench/instruments/adding-pedigrees.md) - [Monitor the Workflow](https://docs.omics.ai/products/workbench/instruments/monitor-the-workflow.md) - [Running Custom Workflows Using Samples](https://docs.omics.ai/products/workbench/instruments/running-custom-workflows-using-samples.md) - [Variant Interpreter](https://docs.omics.ai/products/workbench/variant-interpreter.md) - [Getting Started](https://docs.omics.ai/products/workbench/variant-interpreter/getting-started.md) - [The Data Page](https://docs.omics.ai/products/workbench/variant-interpreter/getting-started/the-data-page.md) - [Opening a sample](https://docs.omics.ai/products/workbench/variant-interpreter/getting-started/opening-a-sample.md) - [The Summary tab & priority findings](https://docs.omics.ai/products/workbench/variant-interpreter/getting-started/the-summary-tab.md) - [Reviewing variants](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants.md) - [Small variants (SNVs & indels)](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/small-variants.md) - [Structural variants](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/structural-variants.md) - [Copy number](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/copy-number.md) - [Tandem repeats](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/tandem-repeats.md) - [Paralogs](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/paralogs.md) - [Filtering & prioritization](https://docs.omics.ai/products/workbench/variant-interpreter/filtering-and-prioritization.md) - [Generating a report](https://docs.omics.ai/products/workbench/variant-interpreter/generating-a-report.md) - [Pipeline & caller versions](https://docs.omics.ai/products/workbench/variant-interpreter/pipeline-and-caller-versions.md) - [Terminology](https://docs.omics.ai/products/workbench/variant-interpreter/terminology.md) - [Entities](https://docs.omics.ai/products/workbench/entities.md) - [Terminology](https://docs.omics.ai/products/workbench/terminology.md) --- # Agent Instructions This documentation is published with GitBook. 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